https://github.com/gersteinlab/texp
TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data
https://github.com/gersteinlab/texp
bioinformatics bioinformatics-pipeline
Last synced: 2 months ago
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TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data
- Host: GitHub
- URL: https://github.com/gersteinlab/texp
- Owner: gersteinlab
- License: apache-2.0
- Created: 2016-09-20T16:23:16.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2019-10-10T14:24:57.000Z (over 5 years ago)
- Last Synced: 2025-01-20T12:07:45.580Z (4 months ago)
- Topics: bioinformatics, bioinformatics-pipeline
- Language: Makefile
- Homepage:
- Size: 39.3 MB
- Stars: 6
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# TeXP
TeXP is a pipeline to evaluate the transcription level of transposable elements in short read RNA-seq data
#About
TeXP is a pipeline for quantifying abundances of Transposable Elements transcripts from RNA-Seq data. TeXP is based on the assumption that RNA-seq reads overlapping Transposable Elements is a composition of pervasive transcription signal and autonomous transcription of Transposable Elements.
https://www.biorxiv.org/content/10.1101/648667v1.full
# How to quickly run TeXP
```
docker run -it fnavarro/texp:latest /bin/bash
```
Download a fastq file from a RNA-seq experiment, for example, MCF-7 from the ENCODE project
```
wget -c -t0 "https://www.encodeproject.org/files/ENCFF000HFF/@@download/ENCFF000HFF.fastq.gz" -O file.fastq.gz
```
Run TeXP
```
./TeXP.sh -f file.fastq.gz -t 1 -o process/example/ -n quick_texp_run
```
The output files will be generated at:
```
ls process/example/quick_texp_run
*.L1HS_hg38.count (Naive counts)
*.L1HS_hg38.count.corrected (Corrected counts)
*.L1HS_hg38.count.rpkm (Naive RPKM)
*.L1HS_hg38.count.rpkm.corrected (Corrected RPKM)
*.L1HS_hg38.count.signal_proportions
```
TIPS:
If fastq files are stored locally you can use
```
docker run -it -v ~/Desktop/:/texp fnavarro/texp:latest /bin/bash
```
To mount "~/Desktop" at your docker container
# Requirements
- Bowtie2 (2.3+)
- Bedtools (2.26+)
- Fastx-toolkit (0.0.14+)
- perl (5.24+)
- python (2.7)
- R (3.3+)
- Penalized package (0.49+)
- samtools (1.3+)
- wgsim (a12da33 on Oct 17, 2011)
---
- Bowtie2 hg38 reference index (http://files2.gersteinlab.org/public-docs/2019/08.14/bowtie2.hg38.tar.bz2)
- Hg38 repetitive element annotation (http://files2.gersteinlab.org/public-docs/2019/08.14/rep_annotation.hg38.tar.bz2)
# Download TeXP
$> git clone https://github.com/gersteinlab/texp.git
Edit TeXP.sh and Update INSTALL_DIR variable to the path where TeXP was cloned
# Installing TeXP dependencies
apt-get update
- Install binaries dependencies
apt-get install -y \
bedtools=2.26.0+dfsg-3 \
bowtie2=2.3.0-2 \
fastx-toolkit=0.0.14-3 \
gawk=1:4.1.4+dfsg-1 \
git \
perl=5.24.1-3+deb9u1 \
python=2.7.13-2 \
r-base=3.3.3-1 \
r-base-dev=3.3.3-1 \
samtools=1.3.1-3 \
wget
- Install Wgsim
mkdir -p /src; \
cd /src ; \
git clone https://github.com/lh3/wgsim.git; \
cd wgsim; \
gcc -g -O2 -Wall -o wgsim wgsim.c -lz -lm; \
mv wgsim /usr/bin/; \
cd /;
- Download Libraries
Fix path (/data/library) to the a proper location at your computation enviroment
mkdir -p /data/library/rep_annotation; \
cd /data/library/rep_annotation; \
wget -c -t0 "http://files2.gersteinlab.org/public-docs/2019/08.14/rep_annotation.hg38.tar.bz2" -O rep_annotation.hg38.tar.bz2; \
tar xjvf rep_annotation.hg38.tar.bz2; \
rm -Rf rep_annotation.hg38.tar.bz2
mkdir -p /data/library/bowtie2; \
cd /data/library/bowtie2; \
wget -c -t0 "http://files2.gersteinlab.org/public-docs/2019/08.14/bowtie2.hg38.tar.bz2" -O bowtie2.hg38.tar.bz2; \
tar xjvf bowtie2.hg38.tar.bz2; \
rm -Rf bowtie2.hg38.tar.bz2
- Install R packages dependencies
echo 'install.packages(c("penalized"), repos="http://cloud.r-project.org", dependencies=TRUE)' > /tmp/packages.R \
&& Rscript /tmp/packages.R
# TeXP config
A few paramaters must be setup so TeXP can properly work outside a docker enviroment; Parameters are set on opts.mk and the user MUST properly set it up.
- LIBRARY_PATH: Absolute path pointing to TeXP library, general this is the path you downloaded TeXP
- EXT_LIBRARY_PATH: Absolute path containing the bowtie2 reference index and Transposable element annotation bed file, downloaded as instructed above
- EXE_DIR: If binaries are found in a single path, EXE_DIR can be used to generalize binary location. For example, if bowtie2, bedtools, etc are located at /usr/bin/, you should set EXE_DIR := /usr
- Dependencies installed in different paths should be defined manually, for example, if wgsim is installed at the home folder, the user must set:
- WGSIM_BIN := ~/wgsim/bin/wgsim
- Finally the user must set to CONFIGURED := TRUE
---
# Docker image
Alternatively, docker images containing all dependencies and libraries can be used. The TeXP docker image also is pre-configured to work outside the box.
Check https://hub.docker.com/r/fnavarro/texp/ for futher instructions:
docker pull fnavarro/texp
---
# Running TeXP
$> ./TeXP.sh -f [FILE_NAME] -t [INT] -o [OUTPUT_PATH] n [SAMPLE_ID]
-f: Input file (fastq,fastq.gz,sra)
-t: Number of threads
-o: Output path (i.e. ./ or ./processed)
-n: Sample name (i.e. SAMPLE01)
---
# FAQ - Frequently Asked Questions
> 1) Does TeXP work for paired end data?
TeXP has been implemented to run one fastq file at a time. Overall, we empirically find that if the RNA-seq library is good, P1 and P2 should yield very similar estimates. Therefore, if using paired-end RNA-seq data, we recommend calculating the mean between both pairs.
> 2) Does TeXP work for unstranded data?
Yes!
> 3) Can I use other aligners
On (figure 15) [https://journals.plos.org/ploscompbiol/article/file?type=supplementary&id=info:doi/10.1371/journal.pcbi.1007293.s015] we show that aligners do not drastically change TeXP estimations, therefore, while you could use other aligners, we suggest using bowtie2 since all TeXP parameterization has been done on bowtie2